RMD (Rice Mutant Database) is an archive for collecting, managing, and searching information of the T-DNA insertion mutants generated by an enhancer trap system. We have generated approximate 129,000 rice mutant (enhancer trap) lines that are now being gathered in the database. Information collected in RMD includes mutant phenotypes, reporter-gene expression patterns, flanking sequences of T-DNA insertional sites, seed availability and others, and can be searched by respective ID, keyword, nucleotide sequence or protein sequence on the website.

compares a nucleotide query sequence against a nucleotide sequence database

tblastn

compares a protein query sequence against a nucleotide sequence database dynamically
translated in all reading frames

tblastx

compares the six-frame translations of a nucleotide query sequence against
the six-frame translations of a nucleotide sequence database.

Q4.FASTA format description

A sequence in FASTA format begins with a single-line description,
followed by lines of sequence data. The description line is
distinguished from the sequence data by a greater-than (">") symbol
in the first column. It is recommended that all lines of text be
shorter than 80 characters in length. An example sequence in FASTA
format is:

Sequences are expected to be represented in the standard IUB/IUPAC amino
acid and nucleic acid codes, with these exceptions: lower-case letters are accepted
and are mapped into upper-case; a single hyphen or dash can be used to represent
a gap of indeterminate length; and in amino acid sequences, U and * are acceptable
letters (see below). Before submitting a request, any numerical digits in the
query sequence should either be removed or replaced by appropriate letter codes
(e.g., N for unknown nucleic acid residue or X for unknown amino acid residue).
The nucleic acid codes supported are:

Restricts the number of short descriptions of matching
sequences reported to the number specified; default
limit is 100 descriptions. See also EXPECT.

ALIGNMENTS

Restricts database sequences to the number specified for
which high-scoring segment pairs (HSPs) are reported;
the default limit is 100. If more database sequences
than this happen to satisfy the statistical
significance threshold for reporting (see EXPECT below),
only the matches ascribed the greatest statistical
significance are reported.

EXPECT

The statistical significance threshold for reporting
matches against database sequences; the default value
is 10, such that 10 matches are expected to be found
merely by chance, according to the stochastic model
of Karlin and Altschul (1990). If the statistical
significance ascribed to a match is greater than the
EXPECT threshold, the match will not be reported.
Lower EXPECT thresholds are more stringent, leading
to fewer chance matches being reported. Fractional
values are acceptable.

Q6.How to obtain seeds or materials in RMD?

Seeds of the enhancer trap lines or mutants in this database can be requested for research purpose by downloading the request form (PDF format) and sending an e-mail to Dr. Changyin
Wu.